Characterization of molecules in nanofluidics

Abstract

Systems are provided for detecting and quantitating short nucleic acid molecules.

What is claimed is: 
     
       1. A method of detecting a tumor cell in a sample comprising polynucleotide sequences, the method comprising:
 labeling a plurality of sequence-specific locations on a polynucleotide sequence of a sample molecule of less than 1000 nucleotides in length; 
 linearizing at least a portion of the sample molecule in a fluidic nanochannel, 
 wherein the fluidic nanochannel has a length of at least 10 nm and cross sectional diameter of less than 1000 nm; 
 quantifying a signal from the labels on the sample molecule; and 
 comparing a quantity of the signal from the sample molecule to a quantity of signal from a reference molecule of less than 1000 nucleotides in length, wherein a difference between the signal of the sample molecule and the signal of the reference molecule is indicative of the presence or absence of a tumor cell in the sample. 
 
     
     
       2. The method of  claim 1 , wherein the sample is derived from a tumor cell, suspected of comprising circulating tumor cells, or derived from a tissue in fluid communication with a tumor cell. 
     
     
       3. The method of  claim 1 , wherein the reference molecule is from a healthy cell. 
     
     
       4. The method of  claim 1 , wherein the quantity of the signal comprises coverage depth. 
     
     
       5. The method of  claim 4 , further comprising generating a histogram distribution to reflect coverage depth for the sample. 
     
     
       6. The method of  claim 1 , wherein the sample molecule and the reference molecule are from different tissues of the same organism. 
     
     
       7. The method of  claim 1 , wherein the labeling comprises labeling the sample molecule with at least two labels located at either end of a zone of interest in the sample molecule. 
     
     
       8. The method of  claim 1 , wherein the quantity of signal from the reference molecule comprises an electronically or optically stored value or set of values. 
     
     
       9. The method of  claim 1 , wherein comparing the quantity of the signal from the sample molecule to the quantity of signal from the reference molecule comprises generating a histogram distribution to reflect coverage depth for the sample. 
     
     
       10. The method of  claim 1 , wherein comparing the quantity of the signal from the sample molecule to the quantity of signal from the reference molecule comprises using the ratio (K) between the signal arising from a plurality of samples or sample portions (S1, S2 . . . Sn) and the signal arising from the reference molecule (C):
     K 1= S 1/ C, K 2= S 2/ C . . . Kn=Sn/C.    
 
     
     
       11. The method of  claim 10 , wherein a difference between K1 and Kn is used to determine the presence of a tumor cell in the sample. 
     
     
       12. The method of  claim 1 , wherein the polynucleotide sequence of the sample molecule comprises less than 550 nucleotides in length. 
     
     
       13. A system for detecting a tumor cell in a sample, comprising:
 a fluidic nanochannel for translocating labeled sample nucleic acid molecules of less than 1000 nucleotides in length, wherein the fluidic nanochannel has a length of at least 10 nm and cross sectional diameter of less than 1000 nm, wherein the fluidic nanochannel is configured to elongate at least a portion of the labeled sample nucleic acid molecules, and wherein the sample nucleic acid molecules are labeled while being less than 1000 nucleotides in length; and 
 a device configured to detect physical counts of signals arising from the labeled sample nucleic acid molecules of less than 1000 nucleotides in length in the fluidic channels. 
 
     
     
       14. The system of  claim 13 , wherein the sample comprises circulating tumor cells, body fluids, or tissues, or is suspected of comprising circulating tumor cells. 
     
     
       15. The system of  claim 13 , wherein the system is configured to correlate signals arising from the labeled sample nucleic acid molecules to signals arising from the corresponding region of a reference molecule. 
     
     
       16. The system of  claim 13 , wherein the signals arising from a known corresponding region of a reference molecule are the signals arising from a labeled reference molecule. 
     
     
       17. The system of  claim 13 , wherein correlating the signals comprises determining the signals arising from a pool of samples or a pool of portions of a sample. 
     
     
       18. The system of  claim 13 , wherein the system is configured to correlate the signals comprises using the ratio (K) between the signal arising from a plurality of samples or sample portions (S1, S2 . . . Sn) and the signal arising from the reference (C):
     K 1= S 1/ C, K 2= S 2/ C . . . Kn=Sn/C.    
 
     
     
       19. The system of  claim 18 , wherein a difference between K1 and Kn is used to determine the presence of a nucleic acid from a tumor cell in the sample. 
     
     
       20. The system of  claim 13 , wherein the system is configured to generate a histogram distribution to reflect coverage depth for the sample. 
     
     
       21. The system of  claim 13 , wherein the detecting comprises optical inspection comprising determining the physical count, the intensity, the wavelength, or the size of the labels, and wherein the detecting comprises optical inspection comprising determining the length of at least one labeled region in the sample.